Defenders from the shadows
by InfinityGamer104
Summary: All Spartan IIs have been resurrected by an unknown force and together with Dr Halsey, Cortana and Senior Chief Petty Officer Franklin Mendez are mysteriously thrown aboard an empty Infinity-class supercarrier and somehow managed to travel to the MCU. With only the Huragok onboard the ship how will they affect the events of the MCU? Little to no romance. Rated T. UP FOR ADOPTION!
1. Prologue

****Summary:**** All Spartan IIs have been resurrected by an unknown force and together with Dr Halsey, Cortana and Senior Chief Petty Officer Franklin Mendez are mysteriously thrown aboard an empty Infinity-class supercarrier and somehow managed to travel to the MCU. With only the Huragok onboard the ship how will they affect the events of the MCU?

 **MUST READ!**

 **A/N: I have 16 Things to mention to avoid confusion.**

 **1\. This is my first story and will now be updated that often since I´m in school.**

 **2\. English is not my main language so the grammar can be a bit wrong.**

 **3\. This story will contain the Avengers, Agents of Shield and Some other Marvel stuff but NOT the X-Men.**

 **4\. Skye/Daisy Johnson from AoS is Secretly allied with the Spartans and has similar training but is unaugmented.**

 **5\. The Infinity-class ship is NOT the same vessel as in Halo 4 and 5(Infinity-101).**

 **6\. The majority of the Spartans will be in cryosleep until needed.**

 **7\. The Spartans age have been reduced from the "unknown force".**

 **8\. The Spartans all have the memories of all the events in the Halo universe until Halo 4, even if they died in the Human-Covenant war. They do have a good relationship with Dr. Halsey and SCPO Mendez. They also ALL have the Mjolnir Mk. 6 Power Armor.**

 **9\. Chef Mendez is a Spartan I in my story though will not see much active combat.**

 **10\. The story will follow canon events until CA:CW as of now.**

 **11\. The Spartans will not go public in the beginning of the story but will monitor the events of the MCU from the shadows and will only have Skye/Daisy in AoS undercover.**

 **12\. After AoU Coulson will contact the Avengers and Skye/Daisy will be the liason between them because she has powers.**

 **13\. This story will NOT have the same layout as "Land of Heroes"**

 **14\. Not any romance that is non-canon, and I will not have Bruce x Natasha. Clint/Hawkeye has his wife Laura.**

 **15\. The unknown force will be investigated and something from the Halo universe may make an appearence.**

 **16\. I will not write the events of Iron Man 1 to The Avengers. It will contain timeskips.**

* * *

 **[3rd Person POV]**

 **Date: ?/?/2557**

In the vast darkness of space there was a single 5.7 kilometer long supercarrier where 33 of humanities best soldiers lay deep frozen in their cryopods. They were not alone though, there were dozens of Huragok in the ship, continuously keeping the ship in optimal condition. They were also accompanied by the UNSC fourth generation Smart A.I. CTN 0452-9 "Cortana", Dr. Catherine Elizabeth Halsey and Senior Cheif Petty Officer Franklin Mendez. The ship was fully stocked with ammunition, firearms, the latest Pelican dropships, fighters and the 10 accompanying Strident-class Heavy Frigates.

The ships resident AI started to wake up to blaring alarms and the sensors were going off the charts. The frist thing the noticed was how much space she had and how fast she could perform her calculations. She then started to reach out in the unknown system she was plugged into and noticed how similar it was to the UNSC Infinity, except for the "cloaking feature". She then gasped when she reached out to the whole system and noticed the 35 cryopods.

"They are all spartans," Cortana thought in shock. She then noticed the two occupants who were not spartans. Her thoughts stopped for a whole 3.564 seconds. "I don´t belive it."

She started the unfreezing process and while she waited for it to finish she explored the ships armaments and crew etc.

 **[Some Time Later]**

The first ones to come out of cryo was Dr. Halsey and Chief Mendez.

Later the rest of the occupants were awake and ready.

Cortana spoke first.

"You are alive" she said. From there on the spartans together with Cortana, Halsey and Mendez started to recall the events of the war and wondering how they could be alive and still have memories of events after they died.

Then Spartan 117 asked the billion dollar question,

"Where are we?"

"We are currently on an Infinity-class supercarrier, and it hasn´t been named yet." Cortana answered.

"So we can go back to Earth?"

"I think so. Why don´t we head up to the bridge?" She suggested.

They proceeded to walk to an elevator and take it up to the bridge, where you could see the darkness of space with no planets in sight.

"We should name the ship." suggested Fred-104, "Master Chief Why don´t you do it?"

 **A/N: Since John-117/Master Chief is the defacto leader of the spartans.**

After a couple of moments of thinking Master Chief said, "UNSC Reach"

"Good choice," said Dr Halsey who had been studying the Huragok, "Now where are we Cortana?"

"It seems we are currently 12,5 lightyears from Earth. It will take approximatley 20 minutes to get there with this forerunner enhanced slipspacedrive." said Cortana.

"Then get us there" Mendez said. Cortana engaged the slipspacedrive and soon the supercarrier accelerated into a vortex of blue and purple colors.

The spartans went to find some quarters to claim as theirs and they then came back just in time for the transition into normal space just outside Pluto in the Sol system.

"Contact HIGHCOM and tell them who we are so we don´t get fired upon." said Chief Mendez.

"I can´t raise them on any channel" said Cortana after a moment of silence.

"This seems rather suspicious," said John-117, "Head towards Earth and see if anything has happened."

"We do have an experimental cloaking feature that we could use" said Cortana to Chief Mendez.

"When we pass Mars engage the cloak and get me a visual on Earth." he decided. While the others had been planning on what to do, Halsey had studied the Huragok and noticed they had installed a translation software into their Mjolnir armor and the tablets so they could now communicate with eachother without the use of handsigns. She informed the others of this new development and watched as Earth came into view and with their cloak engaged noone could detect them.

Everybody gasped as they watched Earth come into view.

"There is no sign of glassing anywhere on the planet!" said Cortana in shock after checking the scanners thousands of times, "There are no orbital platforms but I do detect a large amount of communication from the planet itself."

"Find out what has happened" ordered Chief Mendez earning a 'Yes sir' from Cortana

After a moment of discussion between the spartans and the others Cortana spoke up again.

"This is Earth but not OUR Earth"

* * *

 **A/N: End of prologue, I will try to update once or twice a week with a minimum of 1k words and maybe more. Hope you will enjoy this story.**

 **~ InfinityGamer104**


	2. Chapter 1

****New chapter!****

 **Answers to reviews:**

 **Sparta47: I haven´t watched the X-Men but I have read a lot of fanfictions with them but they have so many characters and they do not exist in the same fictional universe. Marvel studios owns The avengers etc. and 20th Century Fox owns the X-Men and mutants. The X-Men and Avengers co-exist in the comics but not in the movies. Also they will investigate how they got to the MCU but they will not find any explanations.**

 **PocketDuelMonsters: There may be some John x Natasha but the spartans in this story are very strict and tend to stick to the military style and they will not have a civilian identity unless they are on missions. Also John and Natasha will not have a relationship but Natasha will be intrested in John later in the story. Also only Blue Team and some others will be "awake" and the rest will be in cryosleep in the Reach.**

 **Disclaimer: I do NOT own the Avengers, AoS or Halo, they belong to Marvel and 343 Industries.**

* * *

 **[?/?/2013 MCU Time]**

4 years. For 4 years they had been in this strange alternate version of their universe. Much had happened in the world these 4 years, Tony Stark had been kidnapped and became Iron Man, a norse god had come to Earth, a giant green rage moster had wrecked Harlem in New York and there had been an alien invasion that also had occurred in New York.

 **A/N: Strange. Everything is happening in New York. Well, it is called "The city that never sleeps"**

But the world were not the only ones who had been busy, the spartans had also done some stuff. They had researched this strange world and it´s "super heroes" and had made some decisions. Only Blue team was to be out of cryosleep for prolonged periods of time while the rest were in cryo and they were only awakened once a year to be informed if the events of the year so they  
didn´t get confused if they were woken up after several years in cryosleep. The spartans were also confused when they still looked max 20 years old and didn´t age even after being in this world for several years. They hadn´t made a base on the planet and stuck with the UNSC Reach as their base of operations.

Also the Blue team and Cortana had monitored all events in these 4 years and had hacked into every major government agency to find out some information. Meanwhile Dr Halsey had taken a job as a scientist in SHIELD and Chief Mendez was a drill instructor also in SHIELD. While they were there they noticed how they talked about someone hacking into SHIELD and breaking their RSA implementation. They had informed Cortana about this hacker and ordered her to find out who it was because he/she could be an asset or a problem.

That was 1 year ago. They had recruited the hacker, Skye, and made her an undercover agent for them after she received spartan-grade training but, she is of course nowhere near as good as a spartan with their augmentations and experience along with their 8 year long basic training when they were children. Now was the time for her to begin her first assignment.

She was to in some way gain the attention of SHIELD and infiltrate them.

Skye had thought of everything. She had erased all her files and had joined the Rising Tide as part of her cover and had released some of SHIELDs files but she made sure they weren´t the most top secret but it was certain to gain their attention. She had special way to contact Cortana in case of emergency, all you had to do was to type in "CTN 0452-9" in any search engine on any computer or phone and it would open a direct audiolink to Cortana who was disguised as a member of The Department of Homeland Security.

So now the only thing left was to get "captured."

* * *

 **[Timeskip to airplane interrogation]**

"You guys are making a big mistake" said Skye.

"You don´t look that big" answered Agent Ward with a straight face.  
'If only he knew' thought Skye.

"Sorry for the lack of finesse," said agent Coulson, "Agent Ward has had a little history with your group, the Rising Tide."

"I don´t know wha…."tried Skye but was interrupted by Agent Ward.

"Okay there are two ways we can do this"

"Ohh, is one of them the easy way?" asked Skye sarcastically with a grin on her face.

"No" answered Agent Ward with an emotionless voice.

"Oh" said Skye quietly, her grin disappearing and feigning embarrassment.

* * *

The days came and went for Skye, gaining trust from the SHIELD team. The first mission was a bust, she knew Camilla was hiding something the moment she saw her, but of course she couldn´t say that to the team since they wouldn´t belive her or it would raise suspicions. She was forced to save the team by opening a lifeboat inside the "Bus".

Agent Ward had also taken up the task of "training" her but since she already knew the moves he was teaching her it was only a waste of time. She contacted Cortana after a mission if necessary and she had to do some inappropriate actions to make her cover be more real, she couldn´t just be their worst enemy and then be their best friend in a second. While her cover said that she joined the Rising Tide was so she could find out who her parents were and SHIELD had the only clue about them, that´s why she accepted the offer from Coulson, but in reality Cortana had already found out who her partents were and who they are, she hacked in to the redacted document with ease and found out.  
She told Coulson that the document was the reason but the real reason was so he would think she wasn´t hiding anything more and so they could trust her again.

She also had Blue team as backup on every mission and they would be there in a moments notice if needed.

* * *

 **[Timeskip to Fall of SHIELD, ?/?/2014 MCU Time]**

While Cortana had found out about some corrupt files in SHIELD, she didn´t think it would be this deep inside. She had informed Skye of potential undercover agents in SHIELD but was a little bit surprised when Hydra had unveiled themselves and had managed to get more than half of SHIELD infiltrated.

Dr Halsey and Chief Mendez were on their way to the Hub while SHIELD fell and Cortana could easily take over control of their respective Quinjets and have two spartans each waiting to free them when they landed at an random location. Nobody would investigate why 2 insignificant Quinjets disappeared when the worlds largest government agency fell.

Cortana also knew that Director Fury had secret bunkers somwhere on the planet but didn´t know where because they were 'secret'. So when Coulson and Skye´s team had established themselves in the Playground after Grant Ward was revealed to be a Hydra agent she was quite impressed how Fury had managed to hide these bunkers for so long, since some were hidden in plain sight.

* * *

 **A/N End of chapter. This chapter and a bit of the next will be mostly timeskip but after that, after AoU, Skye will be introduced to the Avengers. That´s when the "real" story will begin, with real dialogues and fightscenes.**


	3. Chapter 2 The Avengers

**A/N: Got lots of stuff in school now but will try to update every week once at least.**

 **Didn´t think so many would read my story, thank you all.**

 **Also skye will not meet her parents but the terrigenesis will still be released into the ocean due to unforseen circumstances. Iron Man and Hawkeye will not leave the avengers as the end of AoU says, they will stay. It will be a while before Civil War happens and these missions wont be canon.**

 **I will be using the avengers first names mostly so you don´t get confused.**

 **Disclaimer: I don´t own anything here, it belongs to Marvel and 343 industries.**

* * *

 **[During Age of Ultron movie, ?/?/2015 MCU time]**

Skye was on edge. She was worried that Ultron would find Cortana in the internet since he was a rather sophisticated AI, altough not as advanced as any UNSC Smart AI he was still pretty smart. She had recived a message from Cortana that Blue Team was ready to deploy just incase Ultron was not beaten by the Avengers. Cortana also said that she had found evidence that Coulson was behind the finding of Loki´s scepter and the repairs of Helicarrier No. 64. **(A/N:the one seen in the first avengers movie)**  
Dr. Halsey had also wanted to run a few medical examinations on her about her powers.

Suddenly Mack came up behind her where she was watching live footage of the battle on the screen in the living room.

"Coulson wants you in his office, said it was important"

"I´ll be right up" she answered and turned of the TV.

She walked up to Coulson´s office and knocked.

"Come in" came a Coulson´s voice from inside.

She walked in and sat on the chair in front of his desk.  
She was about to open her mouth to ask why she was called up here when Coulson spoke.

"I have an idea. You don´t have to like it and you don´t have to accept it either but I think it´s pretty good."

"Okay, is it a mission or something because I´m pretty bored after being in quarantine for so long."

"I want you to be a liason between SHIELD and the Avengers" he said. He had Maria Hill with the Avengers but they didn´t know that. He wanted an official liason.

Skye´s mouth dropped open in shock and surprise.

"What?!" she almost screamed.

"I was going to have a liason between them and us and with they better at handling superpowers I thought you would be the perfect one, you have powers and you are an official SHIELD agent." he said calmly, ignoring her outburst.

"I accept on one condition."

"Name it"

"I get to visit he Playground when I want"

"Of course" he said with a smile

* * *

 **[A few days later outside Avengers Compound]**

She was just outside the Avengers compound, ready to go in with Coulson. May had called Natasha Romanoff before she got there and told her about the situation. Natasha was the only one who knew that Coulson was alive and well. She knew she could take on Natasha in hand to hand combat and probably beat her, she didn´t have the augmentations and same long training as the spartans who could easily beat the Avengers any day on the year.

"Skye, only Black Widow knows I´m alive, the rest don´t so be prepared."

"Alright, let´s go in" she said. They opened the doors to Lola and got out.

They walked inside the main doors of the compound when a female voice spoke from all around the room.

" _Welcome to the Avengers compound, my name is FRIDAY and I will guide you to the Avengers personal part of this facility. Ms Romanoff is expecting you."_

"Thank you FRIDAY, it will be most appreciated" thanked Coulson in a proffesional tone.

 **[Avengers POV]**

The Avengers were all in the living room waiting for the new avenger they would receive from the supposedly "new director of SHIELD". Hill had said they could be trusted and they trusted Hills judgment and went with it. Apparently the new avenger had powers she recently discovered and they would help her with it while she helped them on missions and stuff.

They talked until the door opened and an average height, asian-american girl entered the room.  
Behind her a man they thought they would never see again, stood and eyed them carefully. Wanda and Vision had heard about how Coulson had died during the Battle of New York.

Clint Barton was the first to speak.

"Coulson?"

"Yes, it´s me."

"I saw Fury declare you dead. We were at your funeral and everybody mourned you! How are you even alive and why didn´t you tell us?" his voice rose higher and higher till he was almost shouting. He was obviously hurt that his former handler handn´t told him.

"Fury brought me back, and I didn´t tell you because it was protocol. I´m sorry."

Clint and the other Avengers heard how sincere he was and that he really meant it. They had a small "teamtalk" about it, they decided to forgive him.

"We are not happy about that you didn´t tell us but we are glad that you are alive" said Steve with a smile. He had missed Coulson and it was a hard hit for all the Avengers even if they didn´t know him for that long. They talked for a couple of minutes till Coulson spoke to everyone.

"Well it was nice to meet you again, but I´ll have to go now and Skye will introduce herself" Said Coulson and then he walked out of the room.

"Hello" said Skye awkwardly.

"Hello ma'am." said Steve kindly with a small smile. She recived various greetings form the other Avengers.

"You must be tired" said Natasha Romanoff, "Let me show you to your room where you will be staying when you are here."

"Okay" They walked away towards the rooms.

 **[With the Avengers]**

"She´s hot" exclaimed Tony after they left.

"Stark! It´s her first day here, you shouldn´t make her feel uncomfortable." scolded Wanda.

"Did you read her mind?" Clint asked Wanda.

"No, not yet. I didn´t want to invade her privacy." answered Wanda. "I think she can be trusted for now."

"She has hand to hand combat training and can use a gun if I remember what Hill said correctly." said Steve, "her fighting skills and her powers have to be evaluated so we can see her strengths and weaknesses though. We can´t just let her wander off in the field so she can get herself killed."

"We can do that tomorrow, FRIDAY remind Skye that she has to be at the training area at 9 am for evaluations of her combat skills." said Tony

" _Most certainly sir"_ answered FRIDAY.

"Now we watch Disney movies so witchlady here can know what America is." said Tony while turning on the massive TV and some random disney movie started playing. The Avengers made themselves comfortable in the gigantic sofa and watched.

This would be an interesting time for the Avengers and Skye with all her secrets.

* * *

 **A/N: Done, from now on things will be more dialogue and fight scenes. The chapters will most likely also be longer. Also remember this is my first story and I will not be that good at emotional moments and describing fights bu I will do my best. Thanks for reading and see you next time.**


	4. Discontinued

**Important!**

This story has been **discontinued** , but if anyone would like to adopt this story and rewrite it and actually make something out of this I would gladly appreciate it. Although I would like it to have those 16 points that I wrote in the prologue, also, write an explanation for how they got to the MCU and I'd also like to have more detail in the story. The story has to be well written and by someone that actually has the time and will to do so, unlike me.

This story is discontinued because of more important things in my life that take up more time than I have at the moment. I will still read fanfiction and especially if someone decides to adopt this story.

And what I also think would be interesting is if the spartans started a mercenary company, just like in "What just happened" by FunnyGinger08.

It also would be cool if the spartans surprised the avengers with their combat prowess.

AND ONLY LITTLE ROMANCE PLEASE! THIS IS AN ACTION STORY AND I WANT IT TO MOSTLY STAY THAT WAY!

Also, one spartan is THOUGH, he/she can take out atleast half of the avengers by themselves. So don't make the spartans totally underpowered, make it realistic, they were capable of driving back technologically surperior ARMIES for gods sake, so please, all spartans are able to take out at least half of the avengers. Spartans don´t go rogue or AWOL, they have a good team chemistry and the spartans are like a big family even if they seem cold.

And then lastly we have, Skye. Her hand to hand combat is nearly on par with Natasha. She is also capable of using any weapon with excellent efficiency. And she has to be revealed to the Avengers and the AoS team and side with the spartans.

That´s it, please follow these things I have stated above, although, everything is not required.

 **Thank you for all your support and I am grateful that you took your time to read my story!**

 **Happy new year or something, whatever kind of special event you are celebrating, and if you´re not celebrating anything, then have a good day.**


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